Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/GetRandomSubset.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 # Copyright INRA-URGI 2009-2011
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4 #
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 # "http://www.cecill.info".
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10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
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16 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 #
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31 import random
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32 from optparse import OptionParser
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33 from commons.core.parsing.ParserChooser import ParserChooser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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34 from commons.core.writer.TranscriptWriter import TranscriptWriter
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36 from SMART.Java.Python.misc.Progress import Progress
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37
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38 class GetRandomSubset(object):
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39
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40 def __init__(self, verbosity):
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41 self.verbosity = verbosity
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42
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43 def setInputFile(self, fileName, format):
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44 chooser = ParserChooser(self.verbosity)
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45 chooser.findFormat(format)
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46 self.parser = chooser.getParser(fileName)
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47
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48 def setNumber(self, number, percent):
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49 if number != None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 self.number = number
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51 elif percent != None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 self.number = int(float(percent) / 100 * self.parser.getNbTranscripts())
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53 else:
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54 raise Exception("Error! Number of elements to output is not given!")
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55
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56 def setOutputFile(self, fileName):
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57 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
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58
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59 def chooseElements(self):
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60 self.randomIndices = random.sample(range(self.parser.getNbTranscripts()), self.number)
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61
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62 def run(self):
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63 self.chooseElements()
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64 progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
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65 nbWritten = 0
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66 for cpt1, transcript in enumerate(self.parser.getIterator()):
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67 if cpt1 in self.randomIndices:
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68 self.writer.addTranscript(transcript)
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69 nbWritten += 1
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70 progress.inc()
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71 self.writer.write()
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72 self.writer.close()
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73 progress.done()
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74 if self.verbosity > 1:
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75 print "%d transcripts read" % (self.parser.getNbTranscripts())
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76 print "%d transcripts written" % (nbWritten)
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77
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78
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79 if __name__ == "__main__":
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80
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81 description = "Get Random Subset v1.0.1: Get a random sub-set of a list of genomic coordinates. [Category: Personal]"
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82
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83 parser = OptionParser(description = description)
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84 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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85 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
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86 parser.add_option("-n", "--number", dest="number", action="store", default=None, type="string", help="number of elements to output [format: int]")
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87 parser.add_option("-p", "--percent", dest="percent", action="store", default=None, type="string", help="percentage of elements to output (between 0 and 100) [format: int]")
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88 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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89 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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90 (options, args) = parser.parse_args()
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91
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92 grs = GetRandomSubset(options.verbosity)
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93 grs.setInputFile(options.inputFileName, options.format)
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94 grs.setNumber(options.number, options.percent)
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95 grs.setOutputFile(options.outputFileName)
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96 grs.run()